A5016917714- Genetic diversity and population structure
- Sunflower and Safflower Cultivation
- Genomics and Phylogenetic Studies
- Cannabis and Cannabinoid Research
- Plant and animal studies
- Environmental DNA in Biodiversity Studies
- Lichen and fungal ecology
- Genetic Mapping and Diversity in Plants and Animals
- Genetic and Environmental Crop Studies
- Plant-Microbe Interactions and Immunity
- Mycorrhizal Fungi and Plant Interactions
- Chromosomal and Genetic Variations
- Evolution and Genetic Dynamics
- Genetic and phenotypic traits in livestock
- Species Distribution and Climate Change
- Plant Disease Resistance and Genetics
- Soybean genetics and cultivation
- Ecology and Vegetation Dynamics Studies
- Plant Pathogens and Fungal Diseases
- Yeasts and Rust Fungi Studies
- GABA and Rice Research
- Microbial Community Ecology and Physiology
- Plant Parasitism and Resistance
- Botany, Ecology, and Taxonomy Studies
- Plant Virus Research Studies
University of Colorado Boulder
2016-2025
University of Colorado System
2018-2024
Museum of Boulder
2018
Vietnam National University Ho Chi Minh City
2018
University of British Columbia
2007-2017
Color (United States)
2015
Indiana University Bloomington
2004-2009
Indiana University
2008
Brown University
2002-2004
A high-quality reference for the sunflower genome (Helianthus annuus L.) and analysis of gene networks involved in flowering time oil metabolism provide a basis nutritional exploitation analyses adaptation to climate change. Nicolas Langlade colleagues report sequence domesticated sunflower, Helianthus L., global crop that can maintain stable yields across wide range environmental conditions. Their comparative insights into evolutionary history Asterids. They also analysed transcriptomic...
Of the approximately 250,000 species of flowering plants, nearly one in ten are members Compositae (Asteraceae), a diverse family found almost every habitat on all continents except Antarctica. With an origin mid Eocene, is also relatively young with remarkable diversifications during last 40 My. Previous cytologic and systematic investigations suggested that paleopolyploidy may have occurred at least lineage, but recent analysis genomic data was equivocal. We tested for evidence...
Abstract Reproducibility is the benchmark for results and conclusions drawn from scientific studies, but systematic studies on reproducibility of are surprisingly rare. Moreover, many modern statistical methods make use ‘random walk’ model fitting procedures, these inherently stochastic in their output. Does combination procedures current standards data archiving method reporting permit reproduction authors' results? To test this, we reanalysed sets gathered papers using software package...
• Premise of study: To reliably identify lineages below the species level such as subspecies or varieties, we propose an extension to DNA‐barcoding using next‐generation sequencing produce whole organellar genomes and substantial nuclear ribosomal sequence. Because this method uses much longer versions traditional loci in plastid DNA, call our approach ultra‐barcoding (UBC). Methods: We used high‐throughput scan genome generate reliable sequence high copy number regions. Using method,...
Summary Root and rhizosphere microbial communities can affect plant health, but it remains undetermined how domestication may influence these bacterial fungal communities. We grew 33 sunflower ( Helianthus annuus ) strains n = 5) that varied in their extent of assessed root endosphere also the seeds to investigate degree which were influenced by vertical transmission microbiome through seeds. Neither nor affected domestication, did composition In particular, more modern had lower relative...
The data underlying scientific papers should be accessible to researchers both now and in the future, but how best can we ensure that these are available? Here examine effectiveness of four approaches archiving: no stated archiving policy, recommending (but not requiring) archiving, two versions mandating deposition at acceptance. We control for differences between types by trying obtain from use a single, widespread population genetic analysis, structure. At one extreme, found mandated...
Plant species may remain morphologically distinct despite gene exchange with congeners, yet little is known about the genomewide pattern of introgression among species. Here we analyze effects persistent flow on genomic differentiation between sympatric sunflower Helianthus annuus and H. petiolaris. While are strongly isolated in testcrosses, genetic distances at 108 microsatellite loci 14 sequenced genes highly variable much lower (on average) than for more closely related but historically...
Summary The perennial sunflower Helianthus tuberosus , known as Jerusalem Artichoke or Sunchoke, was cultivated in eastern North America before European contact. As such, it represents one of the few taxa that can support an independent origin domestication this region. Its tubers were adopted a source food and forage when species transferred to Old World early 1600s, are still used today. Despite cultural economic importance tuber crop species, its is debated. Competing hypotheses implicate...
Hybridization is a prominent process among natural plant populations that can result in phenotypic novelty, heterosis, and changes gene expression. The effects of intraspecific hybridization on F1 hybrid expression were investigated using parents from divergent, Cirsium arvense, an invasive Compositae weed. Using RNA-seq approach, the 68,746 unigenes was quantified hybrids. levels 51% transcripts differed between parents, majority which had less than 1.25× fold-changes. More higher parent...
Plants of the Cannabis genus are only prolific producers phytocannabinoids, compounds that strongly interact with evolutionarily ancient endocannabinoid receptors shared by most bilaterian taxa. For millennia, plant has been cultivated not for these compounds, but also food, rope, paper, and clothing. Today, specialized varieties yielding high-quality textile fibers, nutritional seed oil, or high cannabinoid content across globe. However, genetic identities histories diverse populations...
Abstract Differential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns genomic differentiation during process speciation. Possible sources reproductive isolation are well studied between coastal and inland subspecies groups Swainson's thrushes, with differences seasonal migratory behaviour likely playing a key role reducing hybrid fitness. We assembled annotated draft reference for this species generated whole‐genome shotgun...
As the most widely used illicit drug worldwide, and as a source of numerous under-studied pharmacologically-active compounds, precise understanding variability in psychological physiological effects Cannabis varieties is essential. The National Institute on Drug Abuse (NIDA) designated sole legal producer for use US research studies. We sought to compare chemical profiles that are available consumers states have state-legalized versus what researchers interested studying plant its effects....
There is increasing evidence that evolution can occur rapidly in response to selection. Recent advances sequencing suggest the possibility of documenting genetic changes as they populations, thus uncovering basis evolution, particularly if samples are available from both before and after Here, we had a unique opportunity directly assess natural populations following an evolutionary fluctuation climate. We analysed genome-wide differences between ancestors descendants Brassica rapa plants two...
Abstract Molecular biologists are rapidly characterizing the genetic basis of flowering in model species such as Arabidopsis thaliana. However, it is not clear how developmental pathways identified controlled environments contribute to variation reproductive timing natural ecological settings. Here we report first study quantitative trait loci (QTL) for date bolting (the transition from vegetative growth) A. thaliana seasonal field and compare results with those obtained under typical...
Genetic variation for quantitative traits is often greater than that expected to be maintained by mutation in the face of purifying natural selection. One possible explanation this observed action heterogeneous selection wild. Here we report on trait loci (QTL) fitness model plant species Arabidopsis thaliana differs among ecological settings and genetic backgrounds. At one QTL, allele enhanced viability fall-germinating seedlings North Carolina reduced fecundity spring-germinating Rhode...
Abstract Here we report the results of an analysis variation at 128 EST-based microsatellites in wild Helianthus annuus, using populations from species' typical plains habitat Kansas and Colorado, as well two arid desert distinct brackish marsh areas Utah. The test statistics lnRV lnRH were used to find regions genome that significantly less variable one population relative others thus are likely contain genes under selection. A small but detectable percentage (1.5–6%) showed evidence for...
Phylogenetic analyses of genes with demonstrated involvement in evolutionary transitions can be an important means resolving conflicting hypotheses about history or process. In sunflower, two have previously been shown to experienced selective sweeps during its early domestication. the present study, we identified a third candidate domestication gene and conducted haplotype all three address recent, controversial hypothesis origin cultivated sunflower. Although scientific consensus had long...
While speciation can be found in the presence of gene flow, it is not clear what impact this flow has on genome- and range-wide patterns differentiation. Here we examine across entire range common sunflower, H. annuus, its historically allopatric sister species argophyllus a more distantly related, sympatric relative petiolaris. Analysis genotypes at 26 microsatellite loci 1015 individuals from three showed substantial introgression between geographically proximal populations annuus...
The role of adaptation in the divergence lineages has long been a central question evolutionary biology, and as multilocus sequence data sets have become available for wide range taxa, empirical estimates levels adaptive molecular evolution are increasingly common. Estimates vary widely among with high Drosophila, bacteria, viruses but very little evidence widespread hominids. Although plants more limited, some recent work suggested that rates plant taxa surprisingly low there is association...
Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding diversity and evolutionary dynamics sunflower (Helianthus annuus L.), especially given its large (∼3.5 Gb) well-documented cases amplification certain transposons within genus, is considerable importance for history this emerging model species. By analyzing approximately 25% random sequence reads assembled bacterial artificial chromosome (BAC) clones, we show that it...
Recent increases in the production of genomic data are yielding new opportunities and challenges for biologists. Among chief problems posed by next-generation sequencing assembly analyses these large sets. Here we present an online server, http://EvoPipes.net, that provides access to a wide range tools bioinformatic oriented ecological evolutionary The EvoPipes.net server includes basic tool kit including sequence cleaning pipeline (SnoWhite), scaffolded software (SCARF), reciprocal...